Stack Exchange Network

Stack Exchange network consists of 175 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [pymol]

a molecular visualization system created by Warren Lyford DeLano. This tag can be used in questions related to the use and the visualizations produced using this software.

3
votes
0answers
76 views

Automating figure-making with PyMOL

What I want to do I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
1
vote
1answer
259 views

Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

I am using pymol to visualise the secondary structure of protein using its cartoon representation. The ...
3
votes
1answer
1k views

How to perform a DNA structural alignment in pymol

How can I "fit" two DNA structures having different nucleotide sequences in PyMol? I would like to use the structure of a DNA-binding protein in PDB (1h9t), which is bound to DNA in the PDB file, ...
3
votes
1answer
2k views

Generate full dimer from monomer with C2 symmetry?

I downloaded a PDB file of a dimer, but it only contains the monomer, and it says that the dimer can be obtained from C2 symmetry. For an example see here: http://www.rcsb.org/pdb/explore/explore.do?...
1
vote
1answer
86 views

Is there a way to see what representations are currently displayed in PyMOL?

I am using PyMol to visualize .pdb protein structures. I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
2
votes
0answers
530 views

Turn off multithreading in pymol [closed]

By default, pymol seems to grab the number of cores on the system for rendering. How can I force it to only use one core? Motivation: I have a large collection ...
14
votes
1answer
1k views

How do I get the current “camera position” in PyMol so I can reuse it in scripts?

I have a few protein models I want to take pictures of with various ligands bound. It would be nice if I could do it from the same "position", but the only way I can figure out to repeat the same ...